Program Director/PI (Last, First, Middle): Shaw, George M. Natural infection by HCV elicits immune responses that in a subset of humans lead to virus containment and elimination. These immune responses may in turn result in enhanced control of subsequent HCV infections. In other subjects, immune responses fail to contain the primary infection leading to viral persistence and disease. Distinguishing the particular immunological features of these different clinical outcomes may provide novel insights into correlates of immune protection and guide rational vaccine design. Projects 1 and 2 of this program project focus on B and T cell responses to the primary infecting virus strain(s) and explore how these immune responses affect the course of subsequent infections. Critical to the success of these studies is an unambiguous molecular identification of HCV strains responsible for acute primary infection and any subsequent infections. Also critical to the success of Projects 1 and 2 is a precise genetic and phenotypic mapping of B cell (neutralizing antibody, nAb) and T cell epitopes on infecting virus strains. Project 3, working in close coordination with Projects 1 and 2, will address these key issues. The specific hypothesis that Project 3 will test is as follows: Single genome sequencing (SGS) of plasma viral RNA (vRNA) will identify and distinguish virus strains responsible for acute primary HCV infection and reinfection and will provide a sensitive and dynamic indicator of host adaptive immune pressures targeting relevant B and T cell viral epitopes. To test this hypothesis, Project 3 will pursue three specific aims: Aim #1: To use single genome sequencing of plasma viral RNA to identify transmitted/founder (T/F) strains of HCV responsible for acute primary infection and reinfection. Aim #2: To determine the dynamics of elimination, replacement, or persistence of transmitted HCV strains in acute and chronic infection and to identify evolutionary pathways and population bottlenecks in the evolving viral quasispecies leading to persistence. Aim #3: To identify sites of immune recognition and selection across the complete HCV envelope (E1E2) gene and viral genome (core through NS5B) targeted by adaptive B and T cell responses. By providing an unambiguous molecular identification of HCV genomes responsible for acute primary infection, and by distinguishing these T/F genomes and their progeny from reinfecting virus strains, Project 3 will enable a precise mapping of B-cell and T-cell epitopes recognized by host immune responses and will facilitate an analysis of immune correlates of protection.